spacedust
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soedinglab
Discovery of conserved gene clusters in multiple genomes
## Expected Behavior Test and obtain the expected gene cluster. ## Current Behavior ### using CDS When I use the gff file generated by prokka, it prompts "Not enough columns...
## Expected Behavior In circular sequences, the last and the first gene in the sequences are neighbors and should be treated as so when searching gene clusters. ## Current Behavior...
## Expected Behavior Fixing the maximal number of threads used. ## Current Behavior Error message "Duplicate parameter --threads" ## Steps to Reproduce (for bugs) Please make sure to execute the...
## Expected Behavior No error. ## Current Behavior ``` Not enough GFF files are provided. Some results might be omitted tmpFolder/15806226240676100088/createsetdb.sh: line 130: 9468 Segmentation fault "${MMSEQS}" gff2db "${@}" "${TMP_PATH}/seqDB"...
I would like to run spacedust on a plasmid database. This database has ~60k individual files that represent separate plasmid "genomes". However when I pass the following command to spacedust:...
Hi, I want to try spacedust and am working on a HPC compute cluster. When I contacted our support team for installation, they told me that, unfortunately, the Github repo...
`spacedust aa2foldseek setDB refFoldseekDB tmpFolder --threads 2` When I was mapping Alphafold database of test protein sequences, the program was always being terminated. Despite trying various methods to reduce the...
comparison accuracy of "spacedust clustersearch" decreases significantly when the targetdb increases
Hi, I found that when the size of the querydb is much smaller than that of the targetdb, it seems that the performance of Spacedust will decrease significantly. My 3...
The paper mentioned that redundant results of over 100 million gene clusters were removed, and then approximately 7,000 non-redundant gene clusters were obtained. However, no corresponding code was found in...
Dear developer Thanks for your such amazing work. Due to firewall restrictions, I cannot download directly using the commands provided by the software. Therefore, I attempted to manually download and...
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Discovery of conserved gene clusters in multiple genomes